Contents
Cellranger Illumina profiling (190c)
## [1] 27998 190
## [1] 27998 186
## [1] 2000
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 186
## Number of edges: 4045
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.7919
## Number of communities: 4
## Elapsed time: 0 seconds
Cellranger Illumina profiling (951c)
## [1] 27998 951
## [1] 27998 935
## [1] 2000
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 935
## Number of edges: 25447
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8540
## Number of communities: 9
## Elapsed time: 0 seconds
Adding Nanopore data (ISOG/ISO)
Gene Markers Heatmap
Correlation between clusters
Clusters re-labelling, saving .rds file
Dotplot
Heatmap
Session Info
sessionInfo()
## R version 3.5.2 (2018-12-20)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 10 (buster)
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so
##
## locale:
## [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
## [5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
## [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] DoubletFinder_2.0.1 metap_1.1 cowplot_1.0.0
## [4] ggrepel_0.8.1 xtable_1.8-4 knitr_1.23
## [7] RColorBrewer_1.1-2 forcats_0.4.0 stringr_1.4.0
## [10] purrr_0.3.2 readr_1.3.1 tidyr_0.8.3
## [13] tibble_2.1.3 ggplot2_3.2.0 tidyverse_1.2.1
## [16] pheatmap_1.0.12 dplyr_0.8.3 Seurat_3.0.2
## [19] BiocStyle_2.10.0
##
## loaded via a namespace (and not attached):
## [1] Rtsne_0.15 colorspace_1.4-1 ggridges_0.5.1
## [4] rstudioapi_0.10 listenv_0.7.0 npsurv_0.4-0
## [7] lubridate_1.7.4 xml2_1.2.0 codetools_0.2-16
## [10] splines_3.5.2 R.methodsS3_1.7.1 lsei_1.2-0
## [13] jsonlite_1.6 broom_0.5.2 ica_1.0-2
## [16] cluster_2.0.7-1 png_0.1-7 R.oo_1.22.0
## [19] sctransform_0.2.0 BiocManager_1.30.4 compiler_3.5.2
## [22] httr_1.4.0 backports_1.1.4 assertthat_0.2.1
## [25] Matrix_1.2-15 lazyeval_0.2.2 cli_1.1.0
## [28] htmltools_0.3.6 tools_3.5.2 rsvd_1.0.1
## [31] igraph_1.2.4.1 gtable_0.3.0 glue_1.3.1
## [34] RANN_2.6.1 reshape2_1.4.3 Rcpp_1.0.1
## [37] cellranger_1.1.0 gdata_2.18.0 ape_5.3
## [40] nlme_3.1-137 gbRd_0.4-11 lmtest_0.9-37
## [43] xfun_0.8 globals_0.12.4 rvest_0.3.4
## [46] irlba_2.3.3 gtools_3.8.1 future_1.14.0
## [49] MASS_7.3-51.1 zoo_1.8-6 scales_1.0.0
## [52] hms_0.4.2 parallel_3.5.2 yaml_2.2.0
## [55] reticulate_1.12 pbapply_1.4-0 gridExtra_2.3
## [58] stringi_1.4.3 caTools_1.17.1.1 bibtex_0.4.2
## [61] Rdpack_0.11-0 SDMTools_1.1-221.1 rlang_0.4.0
## [64] pkgconfig_2.0.2 bitops_1.0-6 evaluate_0.14
## [67] lattice_0.20-38 ROCR_1.0-7 htmlwidgets_1.3
## [70] labeling_0.3 tidyselect_0.2.5 plyr_1.8.4
## [73] magrittr_1.5 bookdown_0.11 R6_2.4.0
## [76] gplots_3.0.1.1 generics_0.0.2 pillar_1.4.2
## [79] haven_2.1.1 withr_2.1.2 fitdistrplus_1.0-14
## [82] survival_2.43-3 future.apply_1.3.0 tsne_0.1-3
## [85] modelr_0.1.4 crayon_1.3.4 KernSmooth_2.23-15
## [88] plotly_4.9.0 rmarkdown_1.13 grid_3.5.2
## [91] readxl_1.3.1 data.table_1.12.2 digest_0.6.20
## [94] R.utils_2.9.0 munsell_0.5.0 viridisLite_0.3.0
